Nathan Spix

I think (hope) this is ready to merge into dev. I did make one substantial plumbing change - for the bismark workflow, I elected to sort the bam immediately after...

@phue Thanks for reviewing! I am sorry about the per-sample genome functionality, I figured it was probably best to at least start with just basic functionality for a first release....

> Yup, Bismark needs BAMs to be sorted by name: https://github.com/FelixKrueger/Bismark/tree/master/Docs#iii-bismark-deduplication-step The previous commits correct this, and also a plumbing issue that was causing `preseq` to fail. I also added...

Hey @sateeshperi thanks so much for checking in! I would love to get this pushed through as well. However, as I am working on it, I've done quite a bit...

Awesome, thank you so much! Yes, I wouldn't mind adding in support for minimap2 as well - better to do it all at once! :)

Hey all, thanks so much for all your hard work on the DSL2 pipeline! Just wanted to note that an alternative to patching the DSL2 module could be a pattern...

Hey @mobilegenome thanks for your interest! Unfortunately I don't have a lot to contribute - most of the previous work on this (I think) was done with bespoke/custom modules, which...

Hey @Emiller88 could you clarify why 1) is incompatible with nf-core modules?? I'm not following you 100%

ok - thank you so much for clarifying!! If i'm understanding correctly, this is the problem that my suggestion [above](https://github.com/nf-core/methylseq/issues/181#issuecomment-1308882396) was designed to address. It's a bit magical (and I...

Yeah it's a pretty nifty feature! I'm not sure about `bismark` and other aligners, but I know that `biscuit` utilizes the reference (not the index, though) for several steps, including...